Chromatin Organization in Glioma Initiation

神经胶质瘤起始中的染色质组织

• 批准号: 10156402
• 负责人: Devin Michael Bready
• 金额: $ 3.78万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-07 至 2024-01-06
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10156402
• 关键词: 3-Dimensional; ATAC-seq; ATRX gene; Address; Adjuvant; Architecture; Astrocytoma; Binding; Biological Assay; Brain; CCCTC-binding factor; CRISPR interference; Cell Cycle; Cell Survival; Cell model; Cells; Characteristics; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; Data; Development; Dioxygenases; Distal; Distal Enhancer Elements; Engineering; Enhancers; Environment; Enzyme Inhibition; Enzymes; Epigenetic Process; Event; Excision; Family; Fellowship; Functional disorder; Genes; Genetic; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Glioblastoma; Glioma; Gliomagenesis; Guide RNA; Histones; Human; Hypermethylation; Impairment; Incidence; Indolent; Intergenic DNA; Isocitrate Dehydrogenase; Lead; Light; Location; Maintenance; Malignant - descriptor; Malignant Neoplasms; Mediating; Metabolism; Modeling; Molecular Conformation; Mutation; Nuclear; Oncogenic; Operative Surgical Procedures; Other Genetics; Pathway interactions; Patients; Pattern; Phenotype; Primary Brain Neoplasms; Production; Publishing; Radiation; Regulation; Reporter; Role; Secondary to; Specimen; TP53 gene; Testing; Transcript; Tumor Suppressor Genes; Tumor Suppressor Proteins; Undifferentiated; Work; XCL1 gene; alpha ketoglutarate; base; cell type; chemotherapeutic agent; epigenome; gain of function mutation; gene interaction; genomic locus; histone demethylase; inhibitor/antagonist; insight; knock-down; mutant; neoplastic cell; nerve stem cell; neurodevelopment; neuroregulation; novel; prevent; promoter; recruit; restoration; sex; small hairpin RNA; stem cell differentiation; stem cell model; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; translocase; treatment strategy; tumor; tumorigenesis; young adult

Project Summary Glioma is the most common primary brain tumor and represents a disproportionate percentage of cancer fatalities in relation to its incidence. In the last decade, it has been discovered that nearly all lower grade gliomas harbor a characteristic gain of function mutation in Isocitrate dehydrogenase I (IDH1) allowing the enzyme to form a novel oncometabolite. These lower grade gliomas invariably progress to high-grade, aggressive glioblastoma. At neither the low-grade nor high-grade stage are directed therapies available and current treatment is limited to surgical resection and adjuvant radiation and alkylating chemotherapeutic agents. Recent efforts have attempted to employ inhibitors of mutant IDH1 to treat these tumors but early evidence is mixed, indicating that mutant IDH1 induces long-lasting epigenetic changes that do not dissipate upon inhibition of the oncometabolite’s production. Studying these tumors has proven difficult compared to IDH wildtype glioma as patient tumors cannot be readily grown in culture. To address this, our group generated a model of low-grade glioma in human neural stem cells (NSCs) which are strongly implicated as the cell of origin for these tumors. This model, referred to as 3- Hit NSCs, reaffirmed previous observations that the IDH1 mutant induces a block to neural precursor differentiation. Strikingly, it revealed that this block to differentiation in NSCs can be completely rescued by restoration of expression of the transcription factor (sex determining region Y)-box 2 (SOX2). Moreover, this reduction of expression and the associated differentiation phenotype occurs secondary to profound changes in 3-dimensional chromatin organization around the SOX2 genomic locus. The proposed work in this fellowship will examine how central these changes in chromatin organization are to the glioma-phenotype in NSCs and will characterize the SOX2 enhancer environment in NSCs to understand its regulation in glioma initiation. Preliminary data suggests that disruption of the SOX2 TAD by preventing binding of the genome organizer CTCF mirrors reduction in SOX2 expression seen in 3-Hit NSCs. Additionally, those regions which lose interaction with the SOX2 promoter in 3-Hit NSCs correlate with regions found to have marks of being active enhancers in other SOX2 expressing cell types. We hypothesize that CTCF eviction in 3-Hit NSCs results in a loss of SOX2 expression through a disruption of promoter interactions with previously uncharacterized enhancers in the SOX2 locus. To evaluate this hypothesis, I will employ complementary and independent approaches that address the involvement of CTCF mediated chromatin architecture dysfunction in glioma initiation, identify novel SOX2 enhancers in NSCs, examine the activity of these enhancers in glioma initiation, and dissect the activity of these enhancers in stem cell differentiation. Finally, I will validate the relevance of these enhancers in glioma by inferring their activity from single cell ATAC-sequencing of surgical low-grade glioma specimens. Through these approaches, paired with the support of the Placantonakis and Skok labs, I will characterize the role of chromatin disorganization in glioma initiation and help understand the developmental and oncogenic regulation of SOX2.

项目摘要 神经胶质瘤是最常见的原发性脑肿瘤， 其发病率。在过去的十年中，已经发现几乎所有的低级别胶质瘤都具有特征性的增加， 异柠檬酸脱氢酶I（IDH 1）的功能突变，允许该酶形成新的癌代谢物。这些较低 恶性胶质瘤总是进展为高恶性、侵袭性胶质母细胞瘤。无论是低级阶段还是高级阶段， 目前的治疗仅限于手术切除和辅助放疗及烷化剂 化疗剂。最近的努力试图采用突变IDH 1的抑制剂来治疗这些肿瘤，但在早期， 证据是混合的，表明突变IDH 1诱导持久的表观遗传变化，在抑制后不会消失 癌代谢物的生产。与IDH野生型胶质瘤相比，研究这些肿瘤已被证明是困难的， 肿瘤不能容易地在培养物中生长。为了解决这个问题，我们的研究小组在人类中建立了一个低级别胶质瘤模型， 神经干细胞（NSC）是这些肿瘤的起源细胞。这一模式被称为3- Hit NSC，重申了先前的观察结果，即IDH 1突变体诱导神经前体分化阻滞。 令人惊讶的是，它揭示了这种对神经干细胞分化的阻断可以通过恢复 转录因子（性别决定区Y）-框2（SOX 2）。此外，这种表达的减少和相关的 分化表型发生继发于SOX 2周围的三维染色质组织的深刻变化 基因座本研究计划的工作将研究这些变化在染色质组织中的重要性 神经胶质瘤表型的神经干细胞，并将在神经干细胞的特点SOX 2增强环境，以了解其调控 在胶质瘤发生中的作用初步数据表明，通过阻止基因组的结合， 组织者CTCF反映了在3次打击NSC中观察到的SOX 2表达的减少。此外，那些失去 与SOX 2启动子的相互作用在3-Hit NSC中与发现具有作为活性增强子的标记的区域相关， 其他表达SOX 2的细胞类型。我们假设CTCF在3次打击的神经干细胞中的清除导致SOX 2表达的丧失 通过破坏启动子与SOX 2基因座中以前未表征的增强子的相互作用。评价 基于这一假设，我将采用互补和独立的方法来解决CTCF介导的参与问题。 神经胶质瘤启动中的染色质结构功能障碍，鉴定NSC中新的SOX 2增强子，检测 这些增强子在胶质瘤起始中的作用，并剖析这些增强子在干细胞分化中的活性。最后要 通过从外科手术的单细胞ATAC测序推断它们的活性来验证这些增强子在胶质瘤中的相关性， 低级别神经胶质瘤样本通过这些方法，再加上Placantonakis和Skok实验室的支持，我将 描述染色质解体在胶质瘤发生中的作用，并帮助理解发育和致癌 SOX 2规范。